knitr::opts_chunk$set(
  echo = TRUE,
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

tidysq

CRAN_Status_Badge Github Actions Build Status codecov.io Lifecycle: experimental

Overview

tidysq contains tools for analysis and manipulation of biological sequences (including amino acid and nucleic acid -- e.g. RNA, DNA -- sequences). Two major features of this package are:

Getting started

Try our quick start vignette or our exhaustive documentation.

Installation

The easiest way to install tidysq package is to download its latest version from CRAN repository:

install.packages("tidysq")

Alternatively, it is possible to download the development version directly from GitHub repository:

# install.packages("devtools")
devtools::install_github("BioGenies/tidysq")

Example usage

library(tidysq)
file <- system.file("examples", "example_aa.fasta", package = "tidysq")
sqibble <- read_fasta(file)
sqibble

sq_ami <- sqibble$sq
sq_ami

# Subsequences can be extracted with bite()
bite(sq_ami, 5:10)

# There are also more traditional functions
reverse(sq_ami)

# find_motifs() returns a whole tibble of useful informations
find_motifs(sqibble, "^VHX")

An example of dplyr integration:

library(dplyr)
# tidysq integrates well with dplyr verbs
sqibble %>%
  filter(sq %has% "VFF") %>%
  mutate(length = get_sq_lengths(sq))

Citation

For citation type:

citation("tidysq")

or use:

Michal Burdukiewicz, Dominik Rafacz, Laura Bakala, Jadwiga Slowik, Weronika Puchala, Filip Pietluch, Katarzyna Sidorczuk, Stefan Roediger and Leon Eyrich Jessen (2021). tidysq: Tidy Processing and Analysis of Biological Sequences. R package version 1.1.3.



michbur/tidysq documentation built on April 1, 2022, 5:18 p.m.